H1N1 is getting a lot of press right now, but remember that, it's a lot of press. Everyday viruses like seasonal flu, colds, gastrointestinal bugs, etc. are prevalent all the time on all surfaces no matter where you go, no matter when. It's just that these everyday, common viruses are just that, everyday and common, not worthy of the media attention. If you're going to catch something, you're going to catch something.
You can do your best to stay healthy by practising good handwashing often, cleaning commonly touched surfaces in hotel rooms as soon as you arrive (I always take lysol or clorox wipes with me and wipe down all the door handles, remotes, phone handset, taps, etc.) and for times in between, carry a travel size bottle of hand sanitizer and remember to use it often, especially before eating.
Go ahead and worry about it, but you're probably more likely to pick something up at home, at the local grocery store or at the movie theater when you're comfortable in your surroundings and you let your guard down. Travelling isn't going to increase your likelihood of catching H1N1 since it's already worldwide.